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sneumann / xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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Excessive amount of warnings from trimMz_Spectrum() #207

Closed sneumann closed 6 years ago

sneumann commented 7 years ago

Hi, as seen on https://travis-ci.org/sneumann/xcms/builds/265836488 , there is an excessive amount of Warnings from trimMz_Spectrum() possibly in case of "mzmin==mzmax". Yours, Steffen

Applying retention time adjustment to the identified chromatographic peaks ... OK
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 279 and 279 for spectrum with acquisition
number 131. Returning empty spectrum.
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 279 and 279 for spectrum with acquisition
...
Warning in trimMz_Spectrum(object, mzlim = mz, msLevel. = msLevel., ...) :
  No data points between 279 and 279 for spectrum with acquisition
number 1278. Returning empty spectrum.
Requesting 176 missing peaks from wt15.CDF ... got 101.
jorainer commented 7 years ago

That warning is kind of OK, since it's thrown if for a certain m/z range no values are present in the mzML file - I guess it comes from chromatogram calls, but am not sure. Have to investigate.

jorainer commented 7 years ago

These warnings seem to be thrown in the vignette.

jorainer commented 6 years ago

Should be fixed in the vignette now. Feel free to reopen if needed.